A persons genetic background plays an important role in their susceptibility to cancer, disease progression, and response to therapy. Genetic variations can be used as markers to understand complex diseases including cancer and AIDS. In collaboration with scientists at the Memorial Sloan Kettering Cancer Institute we have completed a whole genome association study of breast cancer in Ashkenazi Jewish subjects with a family history of disease. The initial scan identified a number of loci with potentially significant associations. From this data we have selected loci for follow up studies in a replication cohort. The <I>TRIM5</I> gene encodes a protein involved in the protection of cells from HIV infection. We have identified regions of the human <I>TRIM5</I> gene that appear to have undergone selection, perhaps in response to previous infection. Other <I>TRIM</I> family sequences in the human genome also appear to have been infected and may be involved in the protection to infection by other viruses. By studying variants in the complement B and C2 (<I>CFH</I>, <I>C2</I>) genes we have identified association in this gene in patients with age-related macular degeneration (AMD). AMD is the leading cause of blindness in the elderly and is estimated to effect as many as of 10 million Americans. By examining the genetic variants in the <I>BF</I> and <I>C2</I> genes significantly protective haplotypes were identified. The complement pathway is important in the response to pathogens causative for cancer. Further study of this important component of the innate immune response could lead to insight into human disease. A deletion that removes the <I>CFHR1</I> gene adjacent to <I>CFH</I> is highly protective for AMD. We have obtained over 3000 DNAs from subjects in the Age-Related Eye Disease Study, and are typing them for the associated markers to understand the details of the association and identify additional loci. The HH/PTCH pathway has been demonstrated to be mutated in virtually all basal cell carcinomas and a portion of medulloblastomas. In addition, many tumors display ligand-dependent activation of the HH/PTCH pathway including pancreas, prostate, gastrointestinal tract, and small cell lung tumors. The steroid-like, natural product molecule cyclopamine specifically binds to SMO, the downstream regulator of the HH/PTCH pathway. Cyclopamine has been shown to inhibit the growth of HH/PTCH-activated cell lines and xenografts. To demonstrate whether cyclopamine inhibits the expression of HH/PTCH target genes we treated prostate (DU-145, LnCaP), gastric (AGS), and breast cancer (SK-BR3) cell lines and confirmed that cyclopamine inhibits proliferation. RNA isolated from treated and untreated DU-145 cells was subjected to quantitative RT-PCR and a reduction in expression of PTCH, SMO, and GLI1, and GLI2 was observed. To further the development of HH/PTCH inhibitors we designed peptides against TM domains and intracellular loops of the SMO protein. SMO is a member of the G-protein-coupled receptor (GPCR) superfamily, and other GPCRs have been targeted by this approach. While peptides against several TM domains failed to have an effect on cell proliferation, peptides against intracellular loops 2 and 3 were potent inhibitors. As with cyclopamine, the active peptides result in a decrease in expression of HH/PTCH target genes. Both cyclopamine and SMO peptides act by eliciting apoptosis, as measured by the TUNEL assay.